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        Note that additional data was saved in [TAG:v29__outrider_external]_multiqc_data when this report was generated.

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        If you use plots from MultiQC in a publication or presentation, please cite:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411
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        Tool Citations

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        To help with this, you can download publication details of the tools mentioned in this report:

        About MultiQC

        This report was generated using MultiQC, version 1.30

        You can see a YouTube video describing how to use MultiQC reports here: https://youtu.be/qPbIlO_KWN0

        For more information about MultiQC, including other videos and extensive documentation, please visit http://multiqc.info

        You can report bugs, suggest improvements and find the source code for MultiQC on GitHub: https://github.com/MultiQC/MultiQC

        MultiQC is published in Bioinformatics:

        MultiQC: Summarize analysis results for multiple tools and samples in a single report
        Philip Ewels, Måns Magnusson, Sverker Lundin and Max Käller
        Bioinformatics (2016)
        doi: 10.1093/bioinformatics/btw354
        PMID: 27312411

        A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.

        Report generated on 2025-07-25, 09:23 CEST based on data in: /data/ceph/ssd/scratch/tmp/wayu0/nf-core-drop-result-core4/work/2a/5601ca8e8f48ccd40c3bfb3d1c8fce

        Number of samples

        Total number of local vs. external samples.

        Showing 2/2 rows.
        sample_typecount
        External
        0
        Local
        10

        Count Quality Control - Mapped vs Counted Reads

        Compares total mapped vs counted reads.

        The Mapped vs Counted Reads plot does not include external counts.

        Consider removing samples with too low or too high size factors.

        Count Quality Control - Size Factors

        Reads Summary Statistics

        Showing 10/10 rows and 3/3 columns.
        RNA_IDReads MappedReads CountedSize Factors
        HG00096
        62349
        37088
        0.9
        HG00103
        58181
        36655
        1.0
        HG00106
        63542
        39291
        1.0
        HG00111
        77674
        49223
        1.2
        HG00116
        61360
        38422
        0.9
        HG00126
        72929
        44651
        1.1
        HG00132
        79999
        49977
        1.2
        HG00149
        66002
        39384
        1.0
        HG00150
        71699
        45629
        1.1
        HG00176
        60056
        37036
        0.8

        Filtering

        Filtering local: A pre-filtered summary of counts using only the local (from BAM) counts. Omitted if no external counts

        all: A pre-filtered summary of counts using only the merged local (from BAM) and external counts

        passed FPKM: Passes the user defined FPKM cutoff in at least 5% of genes

        min 1 read: minimum of 1 read expressed in 5% of genes

        min 10 reads: minimum of 10 reads expressed in 5% of genes.

        Expressed Genes

        Expressed Genes - table

        Showing 10/10 rows and 5/5 columns.
        RNA_IDRankExpressed genesUnion of expressed genesIntersection of expressed genesGenes passed filtering
        HG00096
        3
        117
        133
        99
        133
        HG00103
        8
        123
        157
        96
        157
        HG00106
        10
        125
        161
        95
        161
        HG00111
        7
        122
        152
        97
        152
        HG00116
        1
        112
        112
        112
        112
        HG00126
        6
        120
        147
        97
        147
        HG00132
        4
        119
        140
        98
        140
        HG00149
        9
        124
        159
        95
        159
        HG00150
        5
        119
        145
        97
        145
        HG00176
        2
        114
        123
        103
        123

        Sample Sex Annotation

        Considerations:The verifying of the samples sex is performed by comparing the expression levels of the genes XIST and UTY. In general, females should have high XIST and low UTY expression, and viceversa for males. For it to work, the sample annotation must have a column called ‘SEX’, with values male/female. If some other values exist, e.g., unknown, they will be matched. The prediction is performed via a linear discriminant analysis on the log2 counts.

        Sex column not found in sample annotation

        MultiQC v1.30 - Written by Phil Ewels, available on GitHub.

        This report uses Plotly, jQuery, jQuery UI, Bootstrap and FileSaver.js.